Thanks, fixed in latest commits
https://github.com/kwsch/PKHeX/commit/33649d4e02cbea00ac89dfd7148a190677027852
im pretty sure received flags aren't transmitted anywhere, if you can wait for the next release
that or restore a backup, or hex edit:
offset 0x66200 thru 0x66300 store the 0x800 bitflags in US/UM. For flag 'n', divide it by 8 and add that value to 0x66200 to give you the offset the bitflag is at. You can probably just zero the entire region and resave in PKHeX.